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2 changes: 1 addition & 1 deletion .nojekyll
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4 changes: 2 additions & 2 deletions about.html
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</ul>
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Expand Down Expand Up @@ -995,7 +995,7 @@ <h1 class="title">About</h1>
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<p>Built for the NHS | 2022-2023</p>
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4 changes: 2 additions & 2 deletions anatomy/aml.html
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Expand Down Expand Up @@ -1000,7 +1000,7 @@ <h1 class="title">Azure Machine Learning</h1>
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<p>Built for the NHS | 2022-2023</p>
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4 changes: 2 additions & 2 deletions anatomy/apps.html
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</ul>
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Expand Down Expand Up @@ -1009,7 +1009,7 @@ <h1 class="title">FlowEHR Apps</h1>
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<p>Built for the NHS | 2022-2023</p>
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14 changes: 7 additions & 7 deletions anatomy/feature_store.html
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<h2 data-number="2" class="anchored" data-anchor-id="our-implementation"><span class="header-section-number">2</span> Our implementation</h2>
<p>We store all features in a Microsoft SQL database, and for now have focused on the design of the feature generation pipeline. We have not (yet) implemented separate approaches for realtime time serving (for predictions) and batch serving (for training). As our data volumes and user base grow, we will review this decision.</p>
<p>We chose MSSQL to ensure access to the database for the widest possible community within the NHS.</p>
<p>The feature pipeline is managed by the <a href="https://github.com/UCLH-Foundry/FlowEHR-Data-Forge">Data Forge</a> repository.</p>
<p>The feature pipeline is managed by the <a href="https://github.com/SAFEHR-data/FlowEHR-Data-Forge">Data Forge</a> repository.</p>
<p>The key components of this include:</p>
<dl>
<dt>A pipeline configuration</dt>
<dd>
This defines which features are built, and specifies specific configuration. See <a href="https://github.com/UCLH-Foundry/FlowEHR-Data-Forge/blob/main/patients/pipeline.json">pipeline.json</a>
This defines which features are built, and specifies specific configuration. See <a href="https://github.com/SAFEHR-data/FlowEHR-Data-Forge/blob/main/patients/pipeline.json">pipeline.json</a>
</dd>
<dt>A pipeline trigger</dt>
<dd>
This defines the schedule at which features are updated. See <a href="https://github.com/UCLH-Foundry/FlowEHR-Data-Forge/blob/main/patients/trigger.json">trigger.json</a>.
This defines the schedule at which features are updated. See <a href="https://github.com/SAFEHR-data/FlowEHR-Data-Forge/blob/main/patients/trigger.json">trigger.json</a>.
</dd>
<dt>A per feature entry point</dt>
<dd>
See <a href="https://github.com/UCLH-Foundry/FlowEHR-Data-Forge/blob/main/patients/src/patients/entrypoints/bloodpressure.py">bloodpressure.py</a> that generates a feature for both the latest, and the average blood pressure (where the 24 hour aggregation window is defined in <code>pipeline.json</code>). The are regenerated hourly as per the <code>trigger.json</code> configuration.
See <a href="https://github.com/SAFEHR-data/FlowEHR-Data-Forge/blob/main/patients/src/patients/entrypoints/bloodpressure.py">bloodpressure.py</a> that generates a feature for both the latest, and the average blood pressure (where the 24 hour aggregation window is defined in <code>pipeline.json</code>). The are regenerated hourly as per the <code>trigger.json</code> configuration.
</dd>
<dt>A per feature ‘job’</dt>
<dd>
See <a href="https://github.com/UCLH-Foundry/FlowEHR-Data-Forge/blob/main/patients/src/patients/features/bloodpressure/job.py">bloodpressure/job.py</a> that fetches the source data, splits the text representation <code>120/70</code> into integers for systolic and diastolic pressures,
See <a href="https://github.com/SAFEHR-data/FlowEHR-Data-Forge/blob/main/patients/src/patients/features/bloodpressure/job.py">bloodpressure/job.py</a> that fetches the source data, splits the text representation <code>120/70</code> into integers for systolic and diastolic pressures,
</dd>
</dl>
<p>Each feature is keyed on an identifier for the hospital visit, and the <code>horizon_datetime</code> is the timestamp derived from the trigger against which all these features are anchored.</p>
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4 changes: 2 additions & 2 deletions anatomy/monitoring.html
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4 changes: 2 additions & 2 deletions anatomy/tre.html
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</ul>
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4 changes: 2 additions & 2 deletions faq/azure-anatomy.html
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Expand Down Expand Up @@ -1010,7 +1010,7 @@ <h1 class="title">What’s the difference between Azure, a landing zone, a TRE,
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</ul>
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Expand Down Expand Up @@ -460,7 +460,7 @@ <h1 class="title">How do I contribute to the documentation</h1>
<li>Notebooks and vignettes can just be saved in <code>./docs/notebooks/</code>. Please ensure the first cell in the notebook contains the YAML <a href="https://quarto.org/docs/tools/jupyter-lab.html#yaml-front-matter">metadata</a> for the author, title, and categories.</li>
<li>Quick notes in the style FAQ answers, or ‘today I learned’ notes can be saved into <code>./docs/faq/</code></li>
</ul>
<p>Both will be automatically indexed when the site is deployed. The documentation is deployed using <a href="https://quarto.org">Quarto</a>, and the documentation is built from the <code>./docs/</code> directory. Please fork or clone <a href="https://github.com/UCLH-Foundry/Garden-Path"></a>.</p>
<p>Both will be automatically indexed when the site is deployed. The documentation is deployed using <a href="https://quarto.org">Quarto</a>, and the documentation is built from the <code>./docs/</code> directory. Please fork or clone <a href="https://github.com/SAFEHR-data/Garden-Path"></a>.</p>
<p>You will need to have</p>
<ul>
<li>installed basic python and jupyter extensions necessary including those for jupyter</li>
Expand Down Expand Up @@ -1054,7 +1054,7 @@ <h1 class="title">How do I contribute to the documentation</h1>
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Expand Down Expand Up @@ -995,7 +995,7 @@ <h1 class="title">What is CosmosDB?</h1>
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